Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv26912
Added Files:
molmol-10.5.patch
Log Message:
10.5-specific patch for molmol
--- NEW FILE: molmol-10.5.patch ---
diff -urN molmol_orig/makedef molmol/makedef
--- molmol_orig/makedef 1969-12-31 16:00:00.000000000 -0800
+++ molmol/makedef 2005-05-28 09:44:47.000000000 -0700
@@ -0,0 +1,60 @@
+ TIFFDIR = @PREFIX@/lib
+ MESADIR = $(TOP)/widgets-sgi
+ JPEGDIR = @PREFIX@/lib
+
+ PNGDIR = @PREFIX@/lib
+ ZLIBDIR = /usr/lib
+
+# If you configured any of the above three image formats, uncomment
+# the following four lines, and delete the non-relevant parts if
+# necessary, i. e. if you did not configure all three formats.
+#
+ IMGDEF = -DTIFF_SUPPORT -DJPEG_SUPPORT -DPNG_SUPPORT
+ IMGINCL = -I$(TIFFDIR) -I$(JPEGDIR) -I$(PNGDIR) -I$(ZLIBDIR)
+ IMGLIB = $(TIFFDIR)/libtiff.3.dylib $(JPEGDIR)/libjpeg.dylib \
+ $(PNGDIR)/libpng.dylib $(ZLIBDIR)/libz.dylib
+
+# Some systems do not have the float versions of various math functions,
+# uncomment the following lines if this is the case
+
+ MISSFUNC = -Dsqrtf=sqrt -Dexpf=exp -Dlogf=log \
+ -Dsinf=sin -Dcosf=cos \
+ -Dfabsf=fabs -DMAXINT=INT_MAX
+
+ # -Dceilf=ceil
+
+CPP = /usr/bin/cpp
+
+MCPPFLAGS = -DMAXINT=INT_MAX -I/usr/X11R6/include [EMAIL PROTECTED]@/include
-bind_at_load
+
+CC = /usr/bin/gcc
+
+MCFLAGS = -O -bind_at_load
+
+RANLIB = /usr/bin/ranlib
+
+WAIT = /bin/sleep 2
+
+SHELL = /bin/sh
+
+SGDEVDIR = ogl x11 no pov rib vrml1 vrml2 ps fm
+
+SGDEVDEF = -DSG_DEV_OGL -DSG_DEV_X11 -DSG_DEV_NO -DSG_DEV_POV -DSG_DEV_RIB
-DSG_DEV_VRML1 -DSG_DEV_VRML2 -DSG_DEV_PS -DSG_DEV_CPS -DSG_DEV_FM3 -DSG_DEV_FM4
+
+PUDEVDIR = motif tty
+
+PUDEVDEF = -DPU_DEV_MOTIF -DPU_DEV_TTY
+
+IODEVDIR = motx11 motogl ttyno
+
+IODEVDEF = -DIO_DEV_MOTIF_X11 -DIO_DEV_MOTIF_OGL -DIO_DEV_TTY_NO
+
+
+MOTIFDEF = -DFUNCPROTO
+
+SYSLIB = -L/usr/lib [EMAIL PROTECTED]@/lib -L/usr/X11R6/lib \
+ -lX11 -lXm -lGLU -lGL
/System/Library/Frameworks/OpenGL.framework/Libraries/libGL.dylib
$(MESADIR)/libGLw.a \
+ -lXmu -lXt -lXp -lXpm -lX11 -lXext -lSM -lICE -lm -lc -lmx
+
+TOOLSDIR = $(TOP)/tools
+SGDIR = $(TOP)/sg
diff -urN molmol_orig/molmol molmol/molmol
--- molmol_orig/molmol 2003-01-20 17:44:58.000000000 -0800
+++ molmol/molmol 2005-05-28 09:44:48.000000000 -0700
@@ -1,9 +1,9 @@
-#!/bin/ksh
+#!/bin/zsh
#
# startup script for MOLMOL
#
-MOLMOLHOME=/opt/group/MOLMOL
[EMAIL PROTECTED]@/share/molmol;MOLMOLDEV="Motif/OpenGL"
export MOLMOLHOME
export MOLMOLDEV
@@ -11,55 +11,8 @@
osrel=`uname -r`
osmaj=`echo $osrel | awk -F. '{print $1}'`
osmin=`echo $osrel | awk -F. '{print $2}'`
-localdev=
-glxdev=
-
-if [ $ostype = "IRIX" -o $ostype = "IRIX64" ]; then
- if [ $osmaj -eq 6 -a $osmin -ge 2 -o $osmaj -gt 6 ]; then
- arch=sgi6
- localdev=Motif/OpenGL
- glxdev=Motif/OpenGL
- elif [ $osmaj -eq 5 -a $osmin -ge 3 -o $osmaj -gt 5 ]; then
- arch=sgi5
- localdev=Motif/OpenGL
- glxdev=Motif/OpenGL
- else
- arch=sgi4
- localdev=Motif/GL
- fi
- MONITOR=72HZ; export MONITOR
-elif [ $ostype = "AIX" ]; then
- arch=aix
- localdev=Motif/OpenGL
-elif [ $ostype = "HP-UX" ]; then
- arch=hp
- localdev=Motif/OpenGL
- glxdev=Motif/OpenGL
-elif [ $ostype = "OSF1" ]; then
- arch=dec
- localdev=Motif/OpenGL
-elif [ $ostype = "Linux" ]; then
- arch=lnx
- localdev=Motif/OpenGL
-elif [ $ostype = "SunOS" ]; then
- if [ $osmaj -eq 5 -a $osmin -ge 4 -o $osmaj -gt 5 ]; then
- arch=sol
- localdev=Motif/OpenGL
- else
- arch=sun
- fi
-else
- arch=unknown
-fi
-
-if [ $ostype = "SunOS" ]; then
- xdpy=/usr/openwin/bin/xdpyinfo
-elif [ $ostype = "HP-UX" ]; then
- xdpy=/usr/contrib/bin/X11/xdpyinfo
-else
- xdpy=/usr/bin/X11/xdpyinfo
-fi
-
+localdev=Motif/OpenGL
+glxdev=Motif/OpenGL
printUsage () {
echo "Usage: molmol -ht2as [-o dev] [-r range] [-f macro] files"
echo ""
@@ -209,7 +162,7 @@
fi
if [ "$input" = "-" -o -n "$nograph" ]; then
- $MOLMOLHOME/molmol.$arch $xopt
+ echo "LineBond solid 1 " >>| $startmacro ;
@PREFIX@/share/molmol/src/main/molmol $xopt
else
- $MOLMOLHOME/molmol.$arch $xopt < /dev/null
+ echo "LineBond solid 1 " >>| $startmacro ;
@PREFIX@/share/molmol/src/main/molmol $xopt < /dev/null
fi
diff -urN molmol_orig/molmol.orig molmol/molmol.orig
--- molmol_orig/molmol.orig 1969-12-31 16:00:00.000000000 -0800
+++ molmol/molmol.orig 2005-05-28 09:44:48.000000000 -0700
@@ -0,0 +1,215 @@
+#!/bin/ksh
+#
+# startup script for MOLMOL
+#
+
+MOLMOLHOME=/opt/group/MOLMOL
+export MOLMOLHOME
+export MOLMOLDEV
+
+ostype=`uname`
+osrel=`uname -r`
+osmaj=`echo $osrel | awk -F. '{print $1}'`
+osmin=`echo $osrel | awk -F. '{print $2}'`
+localdev=
+glxdev=
+
+if [ $ostype = "IRIX" -o $ostype = "IRIX64" ]; then
+ if [ $osmaj -eq 6 -a $osmin -ge 2 -o $osmaj -gt 6 ]; then
+ arch=sgi6
+ localdev=Motif/OpenGL
+ glxdev=Motif/OpenGL
+ elif [ $osmaj -eq 5 -a $osmin -ge 3 -o $osmaj -gt 5 ]; then
+ arch=sgi5
+ localdev=Motif/OpenGL
+ glxdev=Motif/OpenGL
+ else
+ arch=sgi4
+ localdev=Motif/GL
+ fi
+ MONITOR=72HZ; export MONITOR
+elif [ $ostype = "AIX" ]; then
+ arch=aix
+ localdev=Motif/OpenGL
+elif [ $ostype = "HP-UX" ]; then
+ arch=hp
+ localdev=Motif/OpenGL
+ glxdev=Motif/OpenGL
+elif [ $ostype = "OSF1" ]; then
+ arch=dec
+ localdev=Motif/OpenGL
+elif [ $ostype = "Linux" ]; then
+ arch=lnx
+ localdev=Motif/OpenGL
+elif [ $ostype = "SunOS" ]; then
+ if [ $osmaj -eq 5 -a $osmin -ge 4 -o $osmaj -gt 5 ]; then
+ arch=sol
+ localdev=Motif/OpenGL
+ else
+ arch=sun
+ fi
+else
+ arch=unknown
+fi
+
+if [ $ostype = "SunOS" ]; then
+ xdpy=/usr/openwin/bin/xdpyinfo
+elif [ $ostype = "HP-UX" ]; then
+ xdpy=/usr/contrib/bin/X11/xdpyinfo
+else
+ xdpy=/usr/bin/X11/xdpyinfo
+fi
+
+printUsage () {
+ echo "Usage: molmol -ht2as [-o dev] [-r range] [-f macro] files"
+ echo ""
+ echo " -h print this message"
+ echo " -t TTY interface (no graphics)"
+ echo " -o name alternate input/output device"
+ echo " -2 stereo mode (OpenGL only)"
+ echo " -a display all atoms instead of backbone"
+ echo " -s superimpose complete backbone"
+ echo " -r range superimpose backbone of given range"
+ echo " -f file execute macro file (- for standard input)"
+ echo " files DG, PDB, Angle or Dump files"
+}
+
+nograph=
+xopt=
+bb=y
+super=
+range=
+input=
+while getopts hto:2asr:f: option; do
+ case $option in
+ h) printUsage
+ exit 0;;
+ t) nograph=y;;
+ 2) xopt=-stereo;;
+ a) bb=;;
+ s) super=y;;
+ r) range=$OPTARG;;
+ f) input=$OPTARG;;
+ o) MOLMOLDEV=$OPTARG;;
+ *) printUsage
+ echo ""
+ echo "passing unknown options to Xt"
+ break;;
+ esac
+done
+shift `expr $OPTIND - 1`
+
+display=$DISPLAY
+
+while [ -n "$*" ]; do
+ case $1 in
+ -bg | -ba*) xopt="$xopt $1 $2"; shift 2;;
+ -bd) xopt="$xopt $1 $2"; shift 2;;
+ -bw | -borderw*) xopt="$xopt $1 $2"; shift 2;;
+ -borderc*) xopt="$xopt $1 $2"; shift 2;;
+ -d*) xopt="$xopt $1 $2"; display=$2; shift 2;;
+ -fg | -for*) xopt="$xopt $1 $2"; shift 2;;
+ -fn | -fon*) xopt="$xopt $1 $2"; shift 2;;
+ -g*) xopt="$xopt $1 $2"; shift 2;;
+ -n*) xopt="$xopt $1 $2"; shift 2;;
+ -t*) xopt="$xopt $1 $2"; shift 2;;
+ -x*) xopt="$xopt $1 $2"; shift 2;;
+ -* | +*) xopt="$xopt $1"; shift;;
+ *) break;;
+ esac
+done
+
+magictmp=/tmp/molmol_magic$$
+
+if [ ! -d $HOME/molmol ]; then
+ mkdir $HOME/molmol
+fi
+startmacro=$HOME/molmol/options.mac
+cp /dev/null $startmacro
+
+if [ -n "$*" ]; then
+ if [ -f $HOME/molmol/dump ]; then
+ mv -f $HOME/molmol/dump $HOME/molmol/dump.old
+ fi
+ echo "0 long 0x3b7a12f9 MOLMOL" > $magictmp
+ echo "0 long 0xf9127a3b MOLMOL" >> $magictmp
+ (
+ for i in $*; do
+ case `file -m $magictmp $i` in
+ *MOLMOL) echo "ReadDump $i"
+ bb=
+ continue;;
+ esac
+ line1=`awk '/^@<TRIPOS>/ {print; exit}; NR > 20 {exit}' $i`
+ case $line1 in
+ @\<TRIPOS\>*) echo "ReadSybyl $i"
+ bb=
+ continue;;
+ esac
+ line1=`awk 'NR == 1; NR > 1 {exit}' $i`
+ case $line1 in
+ \#*) echo "ReadAng $i"
+ continue;;
+ esac
+ line4=`awk 'NR == 4 {print $1}; NR > 4 {exit}' $i`
+ case $line4 in
+ [A-Z]|[A-Z][A-Za-z]) echo "ReadXyz $i"
+ bb=
+ continue;;
+ [A-Z]*) echo "ReadPdb $i"
+ continue;;
+ esac
+ echo "ReadDg $i"
+ done
+ if [ -n "$range" ]; then
+ echo "SelectAtom ':$range && bb'"
+ echo "Fit to_first"
+ echo "SelectAtom ''"
+ fi
+ if [ -n "$super" ]; then
+ echo "SelectAtom 'bb'"
+ echo "Fit to_first"
+ echo "SelectAtom ''"
+ fi
+ if [ -n "$bb" ]; then
+ echo "SelectBond '! bb'"
+ echo "StyleBond invisible"
+ echo "SelectBond 'bb'"
+ fi
+ ) >> $startmacro
+fi
+
+if [ -n "$input" -a "$input" != "-" ]; then
+ if [ -r $input ]; then
+ echo "XMacUser $input" >> $startmacro
+ else
+ echo "XMacStand $input" >> $startmacro
+ fi
+fi
+
+trap "rm -f $startmacro $magictmp" 0 1 2 15
+
+if [ -n "$nograph" ]; then
+ MOLMOLDEV=TTY/NO
+elif [ -n "$MOLMOLDEV" ]; then
+ true # already set
+elif [ -n "$localdev" -a \( $display = ":0" -o $display = ":0.0" \) ]; then
+ MOLMOLDEV=$localdev
+elif [ -x $xdpy ]; then
+ xdpyout=`$xdpy -d $display 2>&1 | egrep 'GLX|unable'`
+ case $xdpyout in
+ *unable*) MOLMOLDEV=TTY/NO
+ nograph=y
+ continue;;
+ *GLX*) if [ -n "$glxdev" ]; then
+ MOLMOLDEV=$glxdev
+ fi
+ continue;;
+ esac
+fi
+
+if [ "$input" = "-" -o -n "$nograph" ]; then
+ $MOLMOLHOME/molmol.$arch $xopt
+else
+ $MOLMOLHOME/molmol.$arch $xopt < /dev/null
+fi
diff -urN molmol_orig/src/iodev/IODev.c molmol/src/iodev/IODev.c
--- molmol_orig/src/iodev/IODev.c 2001-05-27 14:03:30.000000000 -0700
+++ molmol/src/iodev/IODev.c 2005-05-28 11:03:09.000000000 -0700
@@ -44,7 +44,6 @@
#endif
#ifdef IO_DEV_MOTIF_OGL
extern void IOMotifOGLSetDev(void);
-extern void IOMotifOGLDSetDev(void);
#endif
#ifdef IO_DEV_MOTIF_XGL
extern void IOMotifXGLSetDev(void);
@@ -76,7 +75,6 @@
#endif
#ifdef IO_DEV_MOTIF_OGL
{"Motif/OpenGL", IOMotifOGLSetDev},
- {"Motif/OpenGLD", IOMotifOGLDSetDev},
#endif
#ifdef IO_DEV_MOTIF_XGL
{"Motif/XGL", IOMotifXGLSetDev},
diff -urN molmol_orig/src/iodev/IODev.c-dist molmol/src/iodev/IODev.c-dist
--- molmol_orig/src/iodev/IODev.c-dist 1969-12-31 16:00:00.000000000 -0800
+++ molmol/src/iodev/IODev.c-dist 2005-05-28 09:44:50.000000000 -0700
@@ -0,0 +1,149 @@
+/*
+************************************************************************
+*
+* IODev.c - management of I/O devices
+*
+* Copyright (c) 1994
+*
+* ETH Zuerich
+* Institut fuer Molekularbiologie und Biophysik
+* ETH-Hoenggerberg
+* CH-8093 Zuerich
+*
+* SPECTROSPIN AG
+* Industriestr. 26
+* CH-8117 Faellanden
+*
+* All Rights Reserved
+*
+* Date of last modification : 01/05/27
+* Pathname of SCCS file :
/tmp_mnt/net/sn/homeb/rkoradi/molmol-master/src/iodev/SCCS/s.IODev.c
+* SCCS identification : 1.10
+*
+************************************************************************
+*/
+
+#include <stdio.h>
+#include <string.h>
+
+#include <io_dev.h>
+
+#include <sg.h>
+#include <pu_p.h>
+#include <io_error.h>
+
+#ifdef IO_DEV_TTY_NO
+extern void IOTTYNOSetDev(void);
+#endif
+#ifdef IO_DEV_MOTIF_X11
+extern void IOMotifX11SetDev(void);
+#endif
+#ifdef IO_DEV_MOTIF_GL
+extern void IOMotifGLSetDev(void);
+extern void IOMotifGLDSetDev(void);
+#endif
+#ifdef IO_DEV_MOTIF_OGL
+extern void IOMotifOGLSetDev(void);
+extern void IOMotifOGLDSetDev(void);
+#endif
+#ifdef IO_DEV_MOTIF_XGL
+extern void IOMotifXGLSetDev(void);
+#endif
+#ifdef IO_DEV_WIN_OGL
+extern void IOWinOGLSetDev(void);
+extern void IOWinOGLDSetDev(void);
+#endif
+
+IODev *CurrIODevP;
+
+typedef void (*DevSetF) (void);
+
+typedef struct {
+ char *name;
+ DevSetF set;
+} DevListEntry;
+
+static DevListEntry DevList[] = {
+#ifdef IO_DEV_TTY_NO
+ {"TTY/NO", IOTTYNOSetDev},
+#endif
+#ifdef IO_DEV_MOTIF_X11
+ {"Motif/X11", IOMotifX11SetDev},
+#endif
+#ifdef IO_DEV_MOTIF_GL
+ {"Motif/GL", IOMotifGLSetDev},
+ {"Motif/GLD", IOMotifGLDSetDev},
+#endif
+#ifdef IO_DEV_MOTIF_OGL
+ {"Motif/OpenGL", IOMotifOGLSetDev},
+ {"Motif/OpenGLD", IOMotifOGLDSetDev},
+#endif
+#ifdef IO_DEV_MOTIF_XGL
+ {"Motif/XGL", IOMotifXGLSetDev},
+#endif
+#ifdef IO_DEV_WIN_OGL
+ {"Windows/OpenGL", IOWinOGLSetDev},
+ {"Windows/OpenGLD", IOWinOGLDSetDev},
+#endif
+};
+
+IORes
+IOSetDevice(char *devName)
+{
+ int listSize, i;
+
+ listSize = sizeof(DevList) / sizeof(DevList[0]);
+
+ for (i = 0; i < listSize; i++)
+ if (strcmp(DevList[i].name, devName) == 0) {
+ DevList[i].set();
+ PuSetDevice(CurrIODevP->puDevName);
+ SgSetDevice(CurrIODevP->sgDevName);
+ return IO_RES_OK;
+ }
+
+ return IO_RES_ERR;
+}
+
+IORes
+IOInit(char *appName, int *argcP, char *argv[])
+{
+ return CurrIODevP->init(appName, argcP, argv);
+}
+
+IORes
+IOCleanup(void)
+{
+ return CurrIODevP->cleanup();
+}
+
+IORes
+IOSetWindow(PuWindow win)
+{
+ PuSetWindow(win);
+ return CurrIODevP->setWindow(win);
+}
+
+void
+IOEndFrame(void)
+{
+ CurrIODevP->endFrame();
+}
+
+IORes
+IOStartDump(char *format, char *fileName,
+ SgPlotOrient orient, int w, int h, int quality, float gamma)
+{
+ if (CurrIODevP->startDump == NULL) {
+ IORaiseError("dumping of image not supported by IO device");
+ return IO_RES_ERR;
+ }
+
+ return CurrIODevP->startDump(format, fileName, orient, w, h, quality, gamma);
+}
+
+IORes
+IOEndDump(void)
+{
+ return CurrIODevP->endDump();
+}
diff -urN molmol_orig/src/motogl/MotOGL.c molmol/src/motogl/MotOGL.c
--- molmol_orig/src/motogl/MotOGL.c 2000-05-29 09:31:51.000000000 -0700
+++ molmol/src/motogl/MotOGL.c 2005-05-28 09:44:50.000000000 -0700
@@ -31,7 +31,7 @@
#include <Xm/XmStrDefs.h>
#define BOOL MOTIF_BOOL /* hack to avoid naming conflict */
-#include <X11/GLw/GLwMDrawA.h>
+#include <GL/GLwMDrawA.h>
#undef BOOL
#include <sg.h>
diff -urN molmol_orig/src/os/GFile.c molmol/src/os/GFile.c
--- molmol_orig/src/os/GFile.c 2001-06-17 11:59:17.000000000 -0700
+++ molmol/src/os/GFile.c 2005-05-28 11:04:20.000000000 -0700
@@ -38,7 +38,6 @@
const INT32 GFMagic = 0x3b7a12f9;
#ifndef __linux__
-extern char *sys_errlist[];
#endif
extern int errno;
diff -urN molmol_orig/tools/include/values.h molmol/tools/include/values.h
--- molmol_orig/tools/include/values.h 1969-12-31 16:00:00.000000000 -0800
+++ molmol/tools/include/values.h 2005-05-28 09:44:52.000000000 -0700
@@ -0,0 +1,2 @@
+#include <math.h>
+#include <limits.h>
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